Social Networks and Ecological Food Webs

I read an interesting recent article that discussed a digital “autopsy” of the social network Friendster. Friendster was the grandfather of the social network, preceding both MySpace and Facebook. At its peak it had over 100 million users and a $30 million buyout offer from Google (which they turned down). However, following some technical problems and a site redesign in 2009, the network suffered a catastrophic loss of traffic as users moved to other networks like Facebook.

In this “autopsy” the authors looked into the reasons behind Friendsters “death” and discussed two general reasons for the failure:

  1. The first factor is a cost-benefit ratio: when the costs, in terms of time and effort exerted by being a member of the social network are greater than the benefits obtained, the conditions are set for users to leave.
  2. This is where the network’s topology is important. If a huge number of people in the network have only two friends, then when one of them leaves, the other is left alone on the network and will likely exit as well. This results in a cascade of users leaving the network. However, if people have many friends on the network (many connections), the loss of a single friend is unlikely to result in their exit from the network and unlikely to trigger a cascade of exiting users.

The authors concluded that the “cause of death” was due to declining cost-benefit ratios experienced by users as a result of the technical problems and site redesign. However, it was exacerbated by the network structure.

So, the key point here is that the resilience of the network is determined by the number of connections that each person in the network has. So for any given network, the proportion of the network containing a certain number of friends fraction of the network with a certain number of friends with few connections can be a crucial indicator of the network’s overall resilience from cascades.

In ecology, food webs are “networks” that describe a biological community in terms of the interactions between consumers and resources. The interactions are modeled as connections between consumers and resources that relate to the represent the transfer of energy and matter between the two. The interactions are diagrammed as lines connecting the consumers and their resources – which could be predators and prey, herbivores and plants, plants and soil, etc.

What’s interesting about the Friendster article is its very strong parallel to ecological systems like food webs. Both social networks and food webs need many connections for stability and resilience. Like Friendster, food webs with few participants are highly vulnerable to collapse or sudden radical changes in their structure (called a “trophic cascade“), in which the loss or addition of one or more key participants effectively changes the entire food web by altering key links between network participants. (For example, it’s impossible to play the Kevin Bacon game if he were not part of the network).

For social networks, the key to stability is each person having many Friends so that the loss of any single friend from the network is buffered by the many connections that each person has with other friends. For food webs, stability comes from a similar structure: they need many participants in the food web (the network) to create many different pathways between resources. Having many participants requires preserving biodiversity. If the biodiversity of a system is altered too much by the loss of a top predator or the introduction of an invasive species, the “network” can change. When this happens, vital connections between species can be broken and other connections can arise when newly introduced species competes for the same resources that were formerly linked only to native species. If the network does not contain many participants and has few connections, even small changes in the network will have drastic effects – in the worst case, it can result in a trophic cascade, such as the one that “killed” Friendster.


Featured image from:

A Maxent Script Tool for ArcGIS

As part of my PhD research at the University of Arizona where I study biogeography, biodiversity and macroecology, I have been part of a group looking at large-scale biodiversity questions for New World plants. In this role, I have been responsible for generating many species distribution models using Stephen Phillip’s Maxent software (and R with the Dismo package). I also use ArcGIS quite often to prepare environmental data for Maxent modeling, and wanted a way to perform and integrate Maxent modeling into my ArcGIS workflows.

Maxent Tool User InterfaceWhen working with data and analysis, my rule is that if I have to do something complicated more than twice, it’s generally worth it to develop an automated workflow. So for my species distribution modeling needs, I wanted a Maxent script tool that I could use as a standalone geoprocessing tool or embed within a ModelBuilder model for use more complicated workflows. For example, one of my most common workflow is iterating through a list of species and running a species distribution model for each one.

To accomplish this, I wrote an ArcGIS script tool in Python that collects a variety of common Maxent parameters in a typical ArcGIS geoprocessing user interface and populates a command string to execute Stephen Phillip’s maxent.jar Java application via a Python call to execute a system command. The resulting script tool uses the arcpy model, so it works like any other ArcGIS geoprocessing script tool. It can operate as a standalone tool to generate a species distribution model for a single species, or can be placed into a ModelBuilder workflow and linked to input parameters as shown in the example below.

Maxent Tool in a ModelBuilder Model

In this example, the script tool is parameterized with a species occurrence dataset obtained from the iterator object in which each dataset is named genus_species.csv. The tool then generates a species distribution model for each species and saves the model to a separate directory within a designated output directory, naming each directory by the genus and species name specified in the name of the input occurrence dataset.

A partial example of the Python script that obtains the parameters from the input datasets is shown below.

Maxent Tool Python Script

These parameters are then appended to a string object that is a system command call:

myCommand = "java -mx512m -jar \"" + maxent + "\" -e \"" + climatedataFolder + "\""
myCommand += " -s \"" + csvFile + "\" -o \"" + newOutputFolder + "\""
myCommand += " outputformat=" + optOutputFormat.lower() + " outputfiletype=" + optOutputFileType.lower()

Finally the command is executed via a call to the os.system Python interface that executes the maxent.jar Javascript application with the appropriate options:

result = os.system(myCommand)

When the maxent.jar Java application launches, you’ll see the typical Maxent GUI that you would see if you launched maxent.jar directly and ran a model manually. Except in this case the maxent.jar application launches and starts the model automatically, as shown below.:
Maxent Running

Of course there are some additional script lines that are not shown in the examples above add other maxent parameters to the command string and evaluate the result of the os.system call to determine whether the command executed correctly or not.

However, I have placed a copy of a simple ArcGIS Toolbox and the associated Python script in a zipfile that you can download for your own modeling uses at the link below. There are different versions for each version of ArcGIS you may be using. While newer versions of ArcGIS can read older toolboxes, older versions of ArcGIS cannot read newer toolboxes. So be sure to download the file below that is most appropriate for your ArcGIS version.

Maxent Tool in ArcCatalogIf you like the tool, please let me know if you have any questions or comments/ideas. This is a fairly simple first implementation that I built to get through a lot of modeling quickly. However, I have a few ideas for additions to the tool that would enable it to handle species occurrence point data directly (instead of using saved CSVs) and perhaps leverage Maxent cache (.mxe) files instead of using the environmental data ASC files for each model iteration. At the moment, I’m too busy to add these, but it may be something I add in the future to round out the tool better.

Les Miserables Look Down, Look Down the PhD Version

In the opening scene of the new Les Miserables movie, Jean Valjean (played by Hugh Jackman) is one of many shackled prisoners trying pulling a large ship into a dry dock during rough seas. The work song, “Look down, look down” is quite dramatic and the whole scene is cinematically spectacular and a powerful opening to a great film.

After reading the latest edition of PhD Comics’ parody of Les Miserables, I thought back to the opening scene in the movie and the prisoner work song. The song’s parallels with PhD student life were striking.

Thus, in the sprit of the the PhD Comics parody, I present a PhD student version of “Look down, look down”. Apologies to Victor Hugo, and all musical productions of Les Miserables.

Look down, look down
Don’t look em in the eye
Ad-vi-sor comes
Don’t let em see you cry

Look down, look down
Your funding’s gone away
No grant renewed
You’ll have to stay T.A.

Look down, look down
Rejected you have been
Reviewed with scorn
Submission number ten

Look down, look down
Your data seems all wrong
Your test has failed
Your research takes too long

Look down, look down
No correlation here
P value high
This is your greatest fear

Look down, look down
Your findings don’t add up
Reject H-1
Perhaps you should give up

Look down, look down
Your database has crashed
There’s no backup
Your research has been trashed

Look down, look down
Your thesis is a mess
You can’t finish
You might have to confess

Look down, look down
Your research goals not met
One more review
You can’t defend just yet

Look down, look down
Not yet a PhD
May never come
You’re not as good as he

Look down, look down
Five years are all but gone
Too late to quit
You’ll have to carry on

Look down, look down
Don’t look ‘em in the eye
Look down, look down,
You’re here until you die

Creating a Video of Vegetative Cover Sampling

As part of my graduate obligations for a course in methods of measuring and monitoring plant populations, I had to do some type of course project. Though our instructor offered several options of varying difficulty, it was clear that he really wanted someone to attempt to produce a video outlining how to do a method.

As I had done a couple of videos for other projects in the past, I was fairly certain that this would be the most difficult of the graduate project options, but after exploring my other project options, I decided to attempt the video.

So over the last few days I’ve been writing a script, planning shots, doing on-site filming, editing, and voiceover work. Then more on-site filming, more editing and more voiceover work. After several hours of dedicated editing time, I’ve finished the video.

I think it’s pretty good. It’s not great, but it’s got potential. The main challenges were equipment related. It was windy on both filming days and I don’t have fancy microphones, so we had wind noise in some of the live action clips. Despite that I was using an HD video camera that I won at a conference, the video quality wasn’t as good as I’d expected, but it was the best method of filming the video with what we had available.

Anyway, the end-result is an 8 minute video that demonstrates how to sample vegetative cover using the point-intercept method. I briefly walk viewers through what cover is, why it’s commonly measured, and how to establish random sampling locations. Then I illustrate how to lay out a transect and how to sample points using a drop rod. I discuss how to record the data and finish with a demonstration of how the recorded data can be summarized in Excel. (There’s a mistake in that section, that I caught very late in my editing and didn’t want to tackle fixing as it would have required a new voiceover that took me four takes to do the first time. See if you can spot it).

If you’re curious you can find the video on You Tube at:

Feel free to provide comments – as long as they’re positive 😉

Desert Tortoise Training

From this post title, it might appear that I took part in training desert tortoises. In reality I participated in a workshop to learn how to survey, monitor and handle desert tortoises. The 2-day workshop is conducted annually in Ridgecrest, CA by the Desert Tortoise Council and covers a tremendous amount of material including:

  • an overview of desert tortoise taxonomy, life history and threats to its survival
  • information on handling, monitoring, and surveying for desert tortoises
  • authorized egg handling and burrow construction demonstrations

One important fact we learned very early was that based on DNA, geographic, and behavioral differences between desert tortoises populating the areas east and west of the Colorado River, the desert tortoise has been split into two species: Agassiz’s Desert Tortoise (Gopherus agassizii) and Morafka’s Desert Tortoise (Gopherus morafkai).  With G. agassizii occurring in California, Nevada and Utah on the west side of the Colorado River and G. morakfai occurring in Arizona, and the states of Sonora and Sinaloa, Mexico. So, I guess it’s time to update our field guides.

A range map depicting this split can be seen here:

We were also instructed on desert tortoise life history, threats and legal protection.  As the workshop was aimed at biologists who are working to survey, monitor and protect tortoises in the face of development, the workshop included many topics on the laws and legal framework for protection, preservation and take of the species from all of the permitting agencies that we’d potentially be working with (BLM, USFWS, CaDFG, etc.).

Our field sessions included demonstrations on:

  • how to construct protective fencing and shade structures
  • how to construct artificial burrows
  • how to relocate a nest of tortoise eggs
  • how to collect body size and condition data

We also learned how to survey for desert tortoises, including what signs to look for (scat, tracts, geophagy, burrows, etc.) after which we were given the task of surveying a plot that was pre-seeded with tortoise sign.

Finally, Desert Tortoise Council Tortoise Handling Workshops are recognized by the U.S. Fish and Wildlife Service. While a certificate of attendance does not guarantee a USFWS permit, completion of the Workshop should help with the permitting process.

A Species Diversity Map for 88,000 New World Species

This is a small sample of a species diversity map that’s an end product of our models. This was created by overlaying 88,000+ shapefiles and represents the number of species potentially present in each cell. Red is low, dark blue and purple are high (over 8,000 species per cell).

Revisiting the North Etiwanda Preserve

Sage Scrub Chaparral

Sage Scrub Chaparral

When I studied population biology in junior college we conducted our field work in a large expanse of land along the alluvial fan that drained the San Gabriel Mountains to the Inland Empire valley below. Our specific field site was a 750+ acre area containing coastal sage scrub and coastal sage chaparral plant communities that were intersected by riparian corridors of alder, willow and occasionally sycamore trees.

Coastal sage scrub is a type of ecoregion that is located along the southern and central coast of California. It is important because is an endangered ecosystem that contains many unique species that occur nowhere else in the world (endemic), a number of which are endangered species. Coastal sage scrub is imperiled because it is also located on highly valued coastal real estate and threatened by human development.

Coastal sage scrub occurs from sea level to 1500 feet in elevation, along the coastal and inland valley foothills where coastal fog moderates the climate. Habitat contains sparse, low-growing soft, aromatic shrubs that range from dull-green to gray-green in color. In hot, dry summer months, shrubs often lose their leaves and become dormant as an adaptation to drought tolerance. They become green and vibrant again when winter rains arrive.

Some characteristics species in coastal sage scrub communities include:

Federally recognized threatened and endangered species include the California gnatcatcher (Polioptila californica), the San Diego banded gecko (Coleonyx variegatus abbottii ), the cactus wren (Campylorhyncus brunneicapillus), Merriam kangaroo rat (Dipodomys merriami), flannel-mouthed sucker (Catostomus latipinnis), western patch-nosed snake (Salvadora hexalepis), and cheese-weed moth lacewing (Chrysoperla spp.). Thirteen plant species of the coastal sage scrub are also recognized as threatened or endangered. (1)

A few years later the area began rapidly developing and our field area was threatened by a series of housing developments. Through the efforts of many people who fought to see the area protected to stem the decline of chaparral and coastal sage communities, a 762 acre section was set aside as a reserve. The area lies between the developed portions to the south and the national forest to the north and is protected on the southern end by a very wide power transportation corridor that serves as a buffer between the two land uses.

Welcome Sign

Welcome Sign

After several years of being away from this site, I recently revisited it yesterday afternoon and was surprised to see signs pointing the way to the preserve as I drove to the parking area. I was further surprised to see a dozen cars in the parking area at 3 pm on a Tuesday. When I last visited the site, it was protected, but still the completely undeveloped area that few people ever ventured into.

Trail Map

I quickly saw that the preserve has since been enhanced with formal trails, interpretive signs, and a few scattered picnic sites. It was now a popular place for hiking due to its cultural and recreational significance. Many people were taking a new trail that lead to a side canyon that contained a waterfall and shade beneath the alder trees. Others hiked around the lower portion of the preserve stopping at gazebos and interpretive signs.

While it was strange to see so many people in a place I used to walk around without seeing a soul, I was thrilled to see that the plant communities I fondly remembered were still there and appeared to be thriving. Walking through the scrub and chaparral I was transported back in time to my first population biology class, awestruck by the sight and smell of white sage and asking myself the same questions about the distributions of the plants I encountered along my hike.

Walking along one of the trails I saw massive shifts in the vegetation communities along a 1-mile length. Vegetation changed from stands that were dominated by white sage, to stands co-dominated by chemise and buckwheat containing little white sage. Walk a little further and the vegetation became co-dominated by black sage and sagebrush. Along this stretch I could not detect a difference in soil texture or aspect. So the sudden shifts of vegetation may the result of secondary successional processes where fire and floods disturb the vegetation and a different plant community begins growing in the areas that were disturbed. The overall pattern looked like waves of different vegetation along the hillside that was fascinating and worthy of more examination. Some of those communities are shown in the photos below.

Preserve Facing North West

Preserve Facing NW

White Sage

White Sage

White Sage Community

White Sage Community

Chemise and Buckwheat

Chemise and Buckwheat

Black Sage and Sagebrush

Black Sage and Sagebrush

Alder Riparian Woodland

Alder Riparian Woodland

Intersecting what I used to think was scorching hot chaparral (I’ve since lived in Arizona, so I have a new definition of hot) are wonderfully different riparian habitats containing cool, lush, shade tolerant species and – water. Water is a powerful force in these regions, winter rains and spring meltwater can move large amounts of water down the mountain through these canyons. Occasional fires remove vegetation and later rains bring floods that break trees and push large granite boulders downstream too.  These processes cause regular disturbances in the canyons and adjacent lands, and the vegetation is always in some state of recovery. The dense canopy of alder trees in the canyon bottoms is evidence of that those areas were previously disturbed, new trees grew to replace those that were killed, but self-thinning has not yet completed restructuring the tree stand.

Riparian Waterfall

Riparian Waterfall

Alder Woodland

Alder Woodland

The Southern California coastal sage scrub and chaparral communities are a wonderful place to explore with very interesting ecology that is worthy of protection and study. I’m happy that the North Etiwanda Preserve exists and look forward to continued visits.



For more information about the North Etiwanda Preserve see:

Photos of common coastal sage scrub and chaparral plants (from the nearby Cal State San Bernardino campus) can be seen at:

Finally, more information about coastal sage scrub and chaparral can be found at:

Happy exploring !

(1) From:

Night Blooming Cerus, Peniocereus greggii

The Night Blooming Cerus, or Queen of the Night, (Peniocereus greggii) is a Sonoran Desert cactus that most of the year would be virtually impossible to find. It’s main stem is a thin, dull-green to brown stalk that resembles the branch of shrubs like the palo verde, Ironwood, or creosote bushes that it normally grows beneath.

What makes this cactus special is that on certain summer nights the plants in each population produce large blooms synchronously – with some plants producing numerous flowers, some producing one and some none at all. The flowers open at sunset and last for one night, withering in the morning sun.

The flowers are produced only at night, are mostly white, about 3 inches wide and are strongly scented (though some people apparently cannot smell them). The flowers have long floral tubes and are pollinated by hawk moths (Sphingidae) which fly hundreds of yards between different plants in search of nectar. In return they exchange pollen between individuals.

The Night Blooming Cerus is actually not a cerus at all. When cacti were first collected and categorized they were lumped into one genus named ‘Cactus’. Later, taxonomists determined that there were several groups of cacti and split the plants into groups like Opuntia (beaver tail cacti), mammillaria (fish-hook cacti), Cerus (columnar cacti) and others. In the newer classification many columnar cacti were lumped into the Cerus genus, the Night Blooming Cerus being one of them – hence it’s name. However later work further subdivided plants in the Cerus genus into more groups. Columnar cacti like the Giant Saguaro remained in the genus Cerus, but vine-like cacti like the Night Blooming Cerus were moved into a new genus named ‘Peniocerus’, where the species is currently classified.

In Arizona and New Mexico, the Night Blooming Cerus is a protected or endangered species that has seen much of its habitat lost to agricultural and urban development. In addition, its future is dependent upon hawk moths which themselves are vulnerable to impacts from nearby development. For example, where pesticides are heavily used in agricultural areas adjacent to desert habitat, the hawk moth populations can be greatly reduced, such that few remain to pollinate the Night Blooming Cerus to help maintain the cactus’ population size.

Photos from the 2012 Night Bloom at Tohono Chul Park:

All images on this page copyright 2012 by John Donoghue II. All rights reserved.

For more information, see:

Mobile Apps for Naturalists

Project Noah LogoSince nearly everyone carries a smartphone these days, we can now carry a small library worth of field guides with us inside our phones so we never miss an opportunity to identify an interesting organism. With this in mind, here are a few mobile applications that are today’s field ecologist or naturalist should definitely consider having on your smartphone.

Merlin – Merlin is the Cornell Laboratory for Ornithology’s new bird identification app. Answer five simple questions about what bird you’re seeing and Merlin will come up with a list of possibilities based on both the answers to your questions and your location. Merlin is able to make highly educated guesses using its database of more than 70 million observations from the eBird citizen-science project.

Journey North – The Journey North app engages students in a global study of wildlife migration and seasonal change. Focused for K-12 students, users record and submit their observations while they are in the field and share their own field observations with classmates across North America. Students can use the app to track the coming of spring through the migration patterns of monarch butterflies, robins, hummingbirds, whooping cranes, gray whales, bald eagles— and other birds and mammals; the budding of plants; changing sunlight; and other natural events. (iPhone, Android).

BirdLog– I have been wanting a good mobile field notebook application for birding for quite a while. I even went so far as to build my own database to sync between my phone and laptop. BirdLog, is better. Developed in cooperation with the Cornell Lab of Ornithology, BirdLog helps you record and submit your latest bird sightings from the field. Moreover, your sightings contribue to the eBird database and provide data for thousands of amateurs and scientists who study birds. Among its many features, BirdLog allows you to create lists even when there is no cell coverage, keeps a running total of the number of species on your checklist, and plots the exact location of your sightings using your phone’s GPS. (iPhone, Android)

Nature’s Notebook – The National Phenology Network (NPN) has just released the mobile apps for Android and iPhone that let you record phenology (the annual timing of events such as flowering) observations in the field. Fill out a very short form and submit your information for use by scientists everywhere. While many people and applications are set to record when events like flowering start, knowing when they stop is just as important, as it helps tell scientists whether the growing season is getting shorter or shifting. So, one important component of the Nature’s Notebook application is that you can also use it to collect when plants have yet to flower or have stopped flowering, are showing new leaves or have dropped their leaves. (iPhone, Android)

Leafsnap – You can use Leafsnap to help identify plants. Simply use the application to snap a photo of a leaf and it will be uploaded to their servers where sophisticated image recognition software will combine the leaf’s photo with your location (from your phone’s GPS) to suggest possible matching species. (iPhone, Android)

iBird – iBird is the definitive application for identifying birds. It loads the contents of several bird guides onto your phone, combining drawings, photos, recordings of bird calls, range maps and other information to help you lookup any bird and identify its species. iBird loads all of this information on your phone, so you can use it in areas with no internet access. With iBird, there’s really no need to carry a thick bird guide around anymore. (iPhone, Android)

National Audubon Mobile Field Guide Apps – The National Audubon Society offers a suite of applications for smartphones that contain field guides to birds, mammals, reptiles, fish, insects, trees, wildflowers, and mushrooms. (iPhone, Android)

My Nature Animal Tracks – When all you have is evidence that an animal was present, you can use My Nature Animal Tracks to identify the animal by examining their tracks and scat using this handy app. (iPhone)

PhenoMap – Help scientists study changes in phenology (the annual timing of events such as flowering) by snapping photos of when natural plants in your area bloom. Fill out a very short form and upload your sighting to the University of Chicago and the National Phenology Network for inclusion into their phenology database. (iPhone)

ProjectNoah – Earn merit badges for being a citizen scientists and help the larger scientific community by logging your sitings of species in your neighborhood, on trails, etc. The information submitted by tens of thousands of citizen scientists is used to help study species diversity and distributions and other questions. (iPhone, Android)

These are just a few of the many exciting and helpful mobile applications that can assist your field excursions and reduce the number of field manuals you carry. While I’ve tried to introduce some very good and popular applications, this list is by no means complete. If you know an app that should be on this list, please add a comment below.